In the gut contents we found spores of nosema, single-celled fungal parasites that can cause bee dysentery. The spore counts in these and in subsequent samples, however, were not high enough to explain the losses. Molecular analysis of Hackenberg's bees, performed by the other of us (Cox-Foster), also revealed surprising levels of viral infections of various known types. But no single pathogen found in the insects could explain the scale of the disappearance.

In case you weren't aware, and I wasn't for a long time, the foundation in common usage by beekeepers results in much larger bees than what you would find in a natural hive. I've measured sections of natural worker brood comb that are 4.6mm in diameter. This 4.6mm comb was drawn by a hive of commercial Carniolans and this 4.7mm comb was drawn on the first try by a package of commercial Carniolans. What most beekeepers use for worker brood is foundation that is 5.4mm in diameter. If you translate that into three dimensions, instead of one, that produces a bee that is about half again as large as is natural. By letting the bees build natural sized cells, I have virtually eliminated my Varroa and Tracheal mite problems.

The cell size in commercially available combs has been increased over the years to increase the honey yield. (thx, brian)